def getLocalMax(points, groupWidth, adaptiveNoise=False):
"""Get possible peaks from the points using local maxima.
points: (numpy.array) spectrum points
groupWidth: (float) peaks within this range will be grouped together
adaptiveNoise: (bool) calculate noise level separately for each peak
"""
groupWidth /= 2
buff = []
previous = None
localMax = points[0]
growing = True
# get local maxima
for point in points[1:]:
# remember last maximum
if localMax[1] <= point[1]:
localMax = point
growing = True
# store local maximum
elif growing and localMax[1] > point[1]:
# try to group with previous or add new peak
if previous!=None and (localMax[0]-groupWidth)<previous[0]:
if localMax[1] > previous[1]:
buff[-1] = (objects.peak(mz=localMax[0], intensity=localMax[1]))
previous = localMax
else:
buff.append(objects.peak(mz=localMax[0], intensity=localMax[1]))
previous = localMax
localMax = point
growing = False
else:
localMax = point
# get baseline and s/n ratio
noiseLevel, noiseWidth = getNoise(points)
for peak in buff:
if adaptiveNoise:
noiseLevel, noiseWidth = getNoise(points, mz=peak.mz)
peak.baseline = noiseLevel
if noiseWidth != 0:
sn = (peak.intensity-noiseLevel) / noiseWidth
peak.sn = round(sn,3)
return objects.peaklist(buff)
def findPoint(points, mz, adaptiveNoise=False):
"""Find peak for given m/z value.
points: (numpy.array) spectrum points
mz: (float) m/z value
adaptiveNoise: (bool) calculate noise level separately for each peak
"""
# get intensity
i = _getIndex(points, mz)
intensity = _interpolateLine(points[i], points[i-1], mz)
# get noise
if adaptiveNoise:
noiseLevel, noiseWidth = getNoise(points, mz=mz)
else:
noiseLevel, noiseWidth = getNoise(points)
# get S/N
if noiseWidth != 0:
sn = (intensity-noiseLevel) / noiseWidth
sn = round(sn,3)
else:
sn = None
# make peak
if intensity > noiseLevel:
peak = objects.peak(mz=mz, intensity=intensity, baseline=noiseLevel, sn=sn)
return peak
else:
return False
def findPeak(points, mzRange, pickingHeight, adaptiveNoise=False):
"""Find one peak in given m/z range.
points: (numpy.array) spectrum points
mzRange: (list) m/z range where to find the peak
pickingHeight: (float) peak intensity height where the mass is picked in %/100
adaptiveNoise: (bool) calculate noise level separately for each peak
"""
# get current selection
i1 = _getIndex(points, mzRange[0])
i2 = _getIndex(points, mzRange[1])
selection = points[i1:i2]
# get local max for current selection
localMax = [0,0]
for point in selection:
if point[1] > localMax[1]:
localMax = point
# make peak
peak = objects.peak(mz=localMax[0], intensity=localMax[1])
# get centroid
maxWidth = mzRange[1]-mzRange[0]
centroids = getCentroids(points, [peak], pickingHeight, maxWidth, adaptiveNoise)
if centroids:
return centroids[0]
else:
return None
def getSpectrum(self, discrete=False):
"""Get spectrum from document."""
# parse data
data = self._parseData()
if not data:
return False
# parse data as peaklist (discrete points)
if discrete:
for x, p in enumerate(data):
data[x] = objects.peak(p[0], p[1])
spectrum = objects.scan(peaks=data)
# parse data as spectrum (continuous line)
else:
spectrum = objects.scan(points=data)
return spectrum
def getSpectrum(self, discrete=False):
"""Get spectrum from document."""
# parse data
data = self._parseData()
if not data:
return False
# parse data as peaklist (discrete points)
if discrete:
for x, p in enumerate(data):
data[x] = objects.peak(p[0], p[1])
spectrum = objects.scan(peaks=data)
# parse data as spectrum (continuous line)
else:
spectrum = objects.scan(points=data)
return spectrum
def getSpectrum(self, scanNumber=None):
"""Get spectrum from document."""
# init parser
handler = scanHandler(scanNumber)
parser = xml.sax.make_parser()
parser.setContentHandler(handler)
# parse document
try:
document = file(self.path)
parser.parse(document)
document.close()
scan = handler.scan
except stopParsing:
scan = handler.scan
except xml.sax.SAXException:
return False
# check data
if not scan:
return False
# parse peaks
try:
points = self._parsePoints(scan)
except:
return False
# parse data as peaklist (discrete points)
if scan['spectrumType'] == 'discrete':
for x, p in enumerate(points):
points[x] = objects.peak(p[0], p[1])
spectrum = objects.scan(peaks=points)
# parse data as spectrum (continuous line)
else:
spectrum = objects.scan(points=points)
# set metadata
if scan['scanNumber']:
spectrum.scanNumber = int(scan['scanNumber'])
if scan['parentScanNumber']:
spectrum.parentScanNumber = int(scan['parentScanNumber'])
if scan['msLevel']:
spectrum.msLevel = int(scan['msLevel'])
if scan['polarity']:
spectrum.polarity = scan['polarity']
if scan['retentionTime']:
spectrum.retentionTime = scan['retentionTime']
if scan['totIonCurrent']:
spectrum.totIonCurrent = float(scan['totIonCurrent'])
if scan['basePeakMz']:
spectrum.basePeakMZ = float(scan['basePeakMz'])
if scan['basePeakIntensity']:
spectrum.basePeakIntensity = float(scan['basePeakIntensity'])
if scan['precursorMz']:
spectrum.precursorMZ = float(scan['precursorMz'])
if scan['precursorIntensity']:
spectrum.precursorIntensity = float(scan['precursorIntensity'])
return spectrum
def getSpectrum(self, scanNumber=None):
"""Get spectrum from document."""
# init parser
handler = scanHandler(scanNumber)
parser = xml.sax.make_parser()
parser.setContentHandler(handler)
# parse document
try:
document = file(self.path)
parser.parse(document)
document.close()
scan = handler.scan
except stopParsing:
scan = handler.scan
except xml.sax.SAXException:
return False
# check data
if not scan:
return False
# parse peaks
try:
points = self._parsePoints(scan)
except:
return False
# parse data as peaklist (discrete points)
if scan['spectrumType'] == 'discrete':
for x, p in enumerate(points):
points[x] = objects.peak(p[0], p[1])
spectrum = objects.scan(peaks=points)
# parse data as spectrum (continuous line)
else:
spectrum = objects.scan(points=points)
# set metadata
if scan['scanNumber']:
spectrum.scanNumber = int(scan['scanNumber'])
if scan['parentScanNumber']:
spectrum.parentScanNumber = int(scan['parentScanNumber'])
if scan['msLevel']:
spectrum.msLevel = int(scan['msLevel'])
if scan['polarity']:
spectrum.polarity = scan['polarity']
if scan['retentionTime']:
spectrum.retentionTime = scan['retentionTime']
if scan['totIonCurrent']:
spectrum.totIonCurrent = float(scan['totIonCurrent'])
if scan['basePeakMz']:
spectrum.basePeakMZ = float(scan['basePeakMz'])
if scan['basePeakIntensity']:
spectrum.basePeakIntensity = float(scan['basePeakIntensity'])
if scan['precursorMz']:
spectrum.precursorMZ = float(scan['precursorMz'])
if scan['precursorIntensity']:
spectrum.precursorIntensity = float(scan['precursorIntensity'])
return spectrum
